1 Background

2 Set up in R

library(tidyverse); library(patchwork)
## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
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## ✓ readr   2.0.0     ✓ forcats 0.5.1
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## x dplyr::filter() masks stats::filter()
## x dplyr::lag()    masks stats::lag()
library(gt); library(viridis)
## Loading required package: viridisLite
library(plotly)
## 
## Attaching package: 'plotly'
## The following object is masked from 'package:ggplot2':
## 
##     last_plot
## The following object is masked from 'package:stats':
## 
##     filter
## The following object is masked from 'package:graphics':
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##     layout

2.1 Import exisiting data

merged_tax <- read_delim("../microeuks_deepbiosphere_datamine/microeuk-amplicon-survey/data-input/taxonomy.tsv", delim = "\t")
merged_asv <- read_delim("../microeuks_deepbiosphere_datamine/microeuk-amplicon-survey/data-input/microeuk-merged-asv-table.tsv", delim = "\t", skip = 1)
metadata <- read.delim("../microeuks_deepbiosphere_datamine/microeuk-amplicon-survey/data-input/samplelist-metadata.txt")
asv_wtax <- merged_asv %>%
  select(FeatureID = '#OTU ID', everything()) %>%
  pivot_longer(cols = !FeatureID,
               names_to = "SAMPLE", values_to = "value") %>%
  left_join(merged_tax, by = c("FeatureID" = "Feature ID")) %>%
  left_join(metadata) %>%
  filter(!grepl("Siders_", SAMPLE)) %>% 
  filter(SAMPLETYPE != "Incubation") %>% 
  mutate(DATASET = case_when(
    grepl("_GR_", SAMPLE) ~ "GR",
    grepl("Gorda", SAMPLE) ~ "GR",
    grepl("_MCR_", SAMPLE) ~ "MCR",
    grepl("Axial", SAMPLE) ~ "Axial",
  TRUE ~ "Control or blank")) %>%
    separate(Taxon, c("Domain", "Supergroup",
                  "Phylum", "Class", "Order",
                  "Family", "Genus", "Species"), sep = ";", remove = FALSE) %>% 
  unite(SAMPLENAME, SITE, SAMPLETYPE, YEAR, VENT, SAMPLEID, sep = " ", remove = FALSE)

Save to this directory

save(asv_wtax, metadata, file = "data-input/ASVs-18S-survey-03122021.RData")

3 Broad overview of metazoa

load("data-input/ASVs-18S-survey-03122021.RData", verbose = TRUE)
## Loading objects:
##   asv_wtax
##   metadata
# unique(asv_wtax$Supergroup)
# colnames(asv_wtax)
list_of_metazoa <- asv_wtax %>% 
  filter(Supergroup == "Opisthokonta") %>% 
  select(Domain:Species) %>% 
  distinct()
dim(list_of_metazoa)
## [1] 190   8

3.1 Table of all taxa

Output table of all unique metazoan names in dataset.

list_of_metazoa %>% 
  select(-Domain, -Supergroup) %>% 
  arrange(Phylum, Class, Order) %>% 
  gt(
    rowname_col = c("Phylum")
  ) %>% 
  tab_header(title = "Opisthokonta by Phylum")
Opisthokonta by Phylum
Class Order Family Genus Species
Choanoflagellida Choanoflagellatea Acanthoecida Stephanoecidae_Group_D Stephanoecidae_Group_D_X Stephanoecidae_Group_D_X_sp.
Choanoflagellida Choanoflagellatea Acanthoecida NA NA NA
Choanoflagellida Choanoflagellatea Acanthoecida Stephanoecidae_Group_E Stephanoecidae_Group_E_X Stephanoecidae_Group_E_X_sp.
Choanoflagellida Choanoflagellatea Acanthoecida Acanthoecidae_Group_G Acanthoecidae_Group_G_X Acanthoecidae_Group_G_X_sp.
Choanoflagellida Choanoflagellatea Acanthoecida Stephanoecidae_Group_H Stephanoecidae_Group_H_X Stephanoecidae_Group_H_X_sp.
Choanoflagellida Choanoflagellatea Acanthoecida Acanthoecidae_Group_G NA NA
Choanoflagellida Choanoflagellatea Acanthoecida Stephanoecidae_Group_D NA NA
Choanoflagellida Choanoflagellatea Acanthoecida Stephanoecidae_Group_H NA NA
Choanoflagellida Choanoflagellatea Acanthoecida Stephanoecidae_Group_I Stephanoecidae_Group_I_X Stephanoecidae_Group_I_X_sp.
Choanoflagellida Choanoflagellatea Acanthoecida Stephanoecidae_Group_I NA NA
Choanoflagellida Choanoflagellatea Choanoflagellatea_X Choanoflagellatea_X_Group_L Choanoflagellatea_X_Group_L_X Choanoflagellatea_X_Group_L_X_sp.
Choanoflagellida Choanoflagellatea Choanoflagellatea_X Choanoflagellatea_X_Group_P Choanoflagellatea_X_Group_P_X Choanoflagellatea_X_Group_P_X_sp.
Choanoflagellida Choanoflagellatea Choanoflagellatea_X Choanoflagellatea_XX Salpingoeca_XX Salpingoeca_XX_sp.
Choanoflagellida Choanoflagellatea Craspedida NA NA NA
Choanoflagellida Choanoflagellatea Craspedida Monosigidae_Group_O Monosigidae_Group_O_X Monosigidae_Group_O_X_sp.
Choanoflagellida Choanoflagellatea Craspedida Salpingoecidae_Group_C2 Salpingoecidae_Group_C2_X Salpingoecidae_Group_C2_X_sp.
Choanoflagellida Choanoflagellatea Craspedida Monosigidae_Group_B Monosigidae_Group_B_X Monosigidae_Group_B_X_sp.
Choanoflagellida Choanoflagellatea Craspedida Salpingoecidae_Group_C2 NA NA
Choanoflagellida Choanoflagellatea Craspedida Monosigidae_Group_A Monosigidae_Group_A_X Monosigidae_Group_A_X_sp.
Choanoflagellida Choanoflagellatea Craspedida Monosigidae_Group_A NA NA
Choanoflagellida Choanoflagellatea Craspedida Monosigidae_Group_A Monosiga Monosiga_brevicollis
Choanoflagellida Choanoflagellatea Craspedida Monosigidae_Group_A Codosiga Codosiga_sp.
Choanoflagellida Choanoflagellatea Craspedida Monosigidae_Group_A Salpingoeca_A Salpingoeca_A_sp.
Choanoflagellida Choanoflagellatea Craspedida Monosigidae_Group_M Salpingoeca_M Salpingoeca_tuba
Choanoflagellida Choanoflagellatea Craspedida Monosigidae_Group_B NA NA
Choanoflagellida Choanoflagellatea Craspedida Salpingoecidae_Group_C1 Salpingoecidae_Group_C1_X Salpingoecidae_Group_C1_X_sp.
Choanoflagellida Choanoflagellatea NA NA NA NA
Choanoflagellida Choanoflagellida_X Choanoflagellida_XX NA NA NA
Choanoflagellida Choanoflagellida_X Choanoflagellida_XX Choanoflagellida_XXX Choanoflagellida_XXXX Choanoflagellida_XXXX_sp.
Choanoflagellida Choanoflagellida_X Choanoflagellida_XX Choanoflagellida_XX_Clade-2 Choanoflagellida_XX_Clade-2_X Choanoflagellida_XX_Clade-2_X_sp.
Choanoflagellida NA NA NA NA NA
Fungi Ascomycota Pezizomycotina Eurotiomycetes Eurotiomycetes_X Eurotiomycetes_X_sp.
Fungi Ascomycota Pezizomycotina Sordariomycetes Sordariomycetes_X Sordariomycetes_X_sp.
Fungi Ascomycota Pezizomycotina NA NA NA
Fungi Ascomycota Pezizomycotina Pezizomycetes Pezizomycetes_X Pezizomycetes_X_sp.
Fungi Ascomycota Pezizomycotina Dothideomycetes NA NA
Fungi Ascomycota Pezizomycotina Pezizomycotina_X Pezizomycotina_XX Pezizomycotina_XX_sp.
Fungi Ascomycota Pezizomycotina Eurotiomycetes NA NA
Fungi Ascomycota Pezizomycotina Dothideomycetes Verruconis Verruconis_gallopava
Fungi Ascomycota Pezizomycotina Eurotiomycetes Aspergillus NA
Fungi Ascomycota Pezizomycotina Sordariomycetes NA NA
Fungi Ascomycota Pezizomycotina Pezizomycotina_X NA NA
Fungi Ascomycota Pezizomycotina Sordariomycetes Ascotricha NA
Fungi Ascomycota Saccharomycotina Saccharomycetales NA NA
Fungi Ascomycota Saccharomycotina Saccharomycetales Meyerozyma Meyerozyma_guilliermondii
Fungi Ascomycota Saccharomycotina Saccharomycetales Saccharomycetales_X Saccharomycetales_X_sp.
Fungi Ascomycota Saccharomycotina Saccharomycetales Candida NA
Fungi Ascomycota Saccharomycotina Saccharomycetales Saccharomyces NA
Fungi Ascomycota Taphrinomycotina Taphrinomycetes Taphrina NA
Fungi Ascomycota Taphrinomycotina Schizosaccharomycetes Schizosaccharomyces Schizosaccharomyces_japonicus
Fungi Ascomycota Taphrinomycotina Taphrinomycetes NA NA
Fungi Ascomycota Taphrinomycotina Taphrinomycotina_X Saitoella Saitoella_complicata
Fungi Ascomycota NA NA NA NA
Fungi Basidiomycota Agaricomycotina Agaricomycetes Agaricomycetes_X Agaricomycetes_X_sp.
Fungi Basidiomycota Agaricomycotina Agaricomycetes Auricularia Auricularia_auricula-judae
Fungi Basidiomycota Agaricomycotina Agaricomycetes NA NA
Fungi Basidiomycota Agaricomycotina Agaricomycetes Hyphodontia NA
Fungi Basidiomycota Agaricomycotina Tremellomycetes Tremellomycetes_X Tremellomycetes_X_sp.
Fungi Basidiomycota Agaricomycotina Agaricomycetes Pleurotus NA
Fungi Basidiomycota Agaricomycotina Tremellomycetes Trichosporon NA
Fungi Basidiomycota Agaricomycotina Tremellomycetes NA NA
Fungi Basidiomycota Agaricomycotina Agaricomycetes Trichaptum NA
Fungi Basidiomycota Basidiomycota_X Basidiomycota_XX Nephridiophaga Nephridiophaga_blattellae
Fungi Basidiomycota Pucciniomycotina Agaricostilbomycetes NA NA
Fungi Basidiomycota Pucciniomycotina Microbotryomycetes Microbotryomycetes_X Microbotryomycetes_X_sp.
Fungi Basidiomycota Pucciniomycotina NA NA NA
Fungi Basidiomycota Pucciniomycotina Pucciniomycetes NA NA
Fungi Basidiomycota Pucciniomycotina Cystobasidiomycetes Rhodotorula NA
Fungi Basidiomycota Pucciniomycotina Cystobasidiomycetes Rhodotorula Rhodotorula_mucilaginosa
Fungi Basidiomycota Pucciniomycotina Pucciniomycetes Septobasidium NA
Fungi Basidiomycota Pucciniomycotina Cystobasidiomycetes Cystobasidiomycetes_X Cystobasidiomycetes_X_sp.
Fungi Basidiomycota Pucciniomycotina Microbotryomycetes Rhodosporidium NA
Fungi Basidiomycota Pucciniomycotina Cystobasidiomycetes Rhodotorula Rhodotorula_glutinis
Fungi Basidiomycota Pucciniomycotina Cystobasidiomycetes NA NA
Fungi Basidiomycota Pucciniomycotina Cystobasidiomycetes Sporobolomyces Sporobolomyces_roseus
Fungi Basidiomycota Ustilaginomycotina Exobasidiomycetes Exobasidiomycetes_X Exobasidiomycetes_X_sp.
Fungi Basidiomycota Ustilaginomycotina Ustilaginomycetes NA NA
Fungi Basidiomycota Ustilaginomycotina Exobasidiomycetes Malassezia NA
Fungi Blastocladiomycota Blastocladiomycotina Blastocladiomycetes NA NA
Fungi Chytridiomycota Chytridiomycotina Chytridiomycetes NA NA
Fungi Chytridiomycota Chytridiomycotina Chytridiomycetes Chytridiomycetes_X Chytridiomycetes_X_sp.
Fungi Chytridiomycota Chytridiomycotina Chytridiomycetes Rhyzophidiales_X Rhyzophidiales_X_sp.
Fungi Chytridiomycota Chytridiomycotina NA NA NA
Fungi Chytridiomycota Chytridiomycotina Chytridiomycetes Spizellomyces Spizellomyces_sp.
Fungi Chytridiomycota Chytridiomycotina Chytridiomycotina_X Chytridiomycotina_XX Chytridiomycotina_XX_sp.
Fungi Chytridiomycota Chytridiomycotina Chytridiomycetes Spizellomycetales-and-Rhizophlyctidales Spizellomycetales-and-Rhizophlyctidales_sp.
Fungi Chytridiomycota Chytridiomycotina Chytridiomycetes Phlyctochytrium Phlyctochytrium_planicorne
Fungi Cryptomycota Cryptomycotina Cryptomycotina_X Cryptomycotina_XX Cryptomycotina_XX_sp.
Fungi Fungi_X Fungi_XX Fungi_XXX Fungi_XXXX Fungi_XXXX_sp.
Fungi Fungi_X Fungi_XX Fungi_XXX NA NA
Fungi Microsporidiomycota Microsporidiomycotina Microsporidiomycotina_X Microsporidium Microsporidium_sp.
Fungi Microsporidiomycota Microsporidiomycotina Microsporidiomycotina_X Facilispora Facilispora_margolisi
Fungi Mucoromycota Mucoromycotina Mucoromycotina_X Mortierella Mortierella_wolfii
Fungi Mucoromycota Mucoromycotina Mucoromycotina_X Mucoromycotina_XX Mucoromycotina_XX_sp.
Fungi Mucoromycota Mucoromycotina Mucoromycotina_X NA NA
Fungi NA NA NA NA NA
Mesomycetozoa Ichthyosporea Ichthyosphonida Ichthyophonidae_Amoebidianae NA NA
Mesomycetozoa Ichthyosporea Ichthyosphonida NA NA NA
Mesomycetozoa Ichthyosporea Ichthyosphonida Pseudoperkinsidae NA NA
Mesomycetozoa Ichthyosporea Ichthyosphonida Abeoformidae_Group_MAIP_2 Abeoformidae_Group_MAIP_2_X Abeoformidae_Group_MAIP_2_X_sp.
Mesomycetozoa Ichthyosporea Rhynosporida NA NA NA
Metazoa Annelida Annelida_X Annelida_XX NA NA
Metazoa Annelida Annelida_X Annelida_XX Paralvinella NA
Metazoa Annelida Annelida_X Siboglinidae NA NA
Metazoa Annelida Annelida_X Annelida_XX Vigtorniella Vigtorniella_sp.
Metazoa Annelida Annelida_X Annelida_XX Protodrilus NA
Metazoa Arthropoda Chelicerata Arachnida NA NA
Metazoa Arthropoda Chelicerata Pycnogonida NA NA
Metazoa Arthropoda Crustacea Maxillopoda NA NA
Metazoa Arthropoda Crustacea Maxillopoda Maxillopoda_X Maxillopoda_X_sp.
Metazoa Arthropoda Crustacea Ostracoda NA NA
Metazoa Arthropoda Crustacea Maxillopoda Calocalanus Calocalanus_sp.
Metazoa Arthropoda Crustacea Malacostraca NA NA
Metazoa Arthropoda Crustacea Maxillopoda Clausocalanus Clausocalanus_furcatus
Metazoa Arthropoda Crustacea Maxillopoda Oithona Oithona_sp.
Metazoa Arthropoda Crustacea Maxillopoda Metridia Metridia_sp.
Metazoa Arthropoda Crustacea Maxillopoda Eudiaptomus Eudiaptomus_sp.
Metazoa Arthropoda Hexapoda Insecta NA NA
Metazoa Bryozoa Bryozoa_X Bryozoa_XX NA NA
Metazoa Chaetognatha Aphragmophora Aphragmophora_X NA NA
Metazoa Cnidaria Cnidaria_X Hydrozoa NA NA
Metazoa Cnidaria Cnidaria_X Scyphozoa NA NA
Metazoa Cnidaria Cnidaria_X Hydrozoa Hydrozoa_X Hydrozoa_X_sp.
Metazoa Cnidaria Cnidaria_X Hydrozoa Apolemia Apolemia_sp.
Metazoa Cnidaria Cnidaria_X Anthozoa Nematostella Nematostella_vectensis
Metazoa Cnidaria Cnidaria_X Anthozoa NA NA
Metazoa Cnidaria Cnidaria_X Hydrozoa Zanclea Zanclea_sp.
Metazoa Cnidaria Cnidaria_X Hydrozoa Cordagalma Cordagalma_cordiforme
Metazoa Cnidaria Cnidaria_X Scyphozoa Atolla NA
Metazoa Cnidaria Cnidaria_X Hydrozoa Clytia NA
Metazoa Cnidaria Cnidaria_X Scyphozoa Phacellophora NA
Metazoa Cnidaria Cnidaria_X Scyphozoa Cyanea NA
Metazoa Cnidaria Cnidaria_X Scyphozoa Aurelia NA
Metazoa Craniata Craniata_X Teleostei NA NA
Metazoa Craniata Craniata_X Lepidosauria Scincus Scincus_scincus
Metazoa Craniata Craniata_X Mammalia NA NA
Metazoa Craniata Craniata_X Teleostei Auxis Auxis_rochei
Metazoa Craniata Craniata_X Teleostei Salmo Salmo_salar
Metazoa Craniata Craniata_X Mammalia Homo Homo_sapiens
Metazoa Ctenophora Ctenophora_X Ctenophora_XX NA NA
Metazoa Ctenophora Ctenophora_X Ctenophora_XX Beroe NA
Metazoa Ctenophora Ctenophora_X Ctenophora_XX Ctenophora_XXX Ctenophora_XXX_sp.
Metazoa Echinodermata Echinodermata_X Echinodermata_XX NA NA
Metazoa Echinodermata Echinodermata_X Echinodermata_XX Xyloplax Xyloplax_janetae
Metazoa Gastrotricha Gastrotricha_X Gastrotricha_XX NA NA
Metazoa Hemichordata Hemichordata_X Hemichordata_XX NA NA
Metazoa Loricifera Loricifera_X Loricifera_XX Pliciloricus Pliciloricus_sp.
Metazoa Mesozoa Mesozoa_X Orthonectida Rhopalura Rhopalura_ophiocomae
Metazoa Metazoa_X Metazoa_XX Metazoa_XXX Metazoa_XXXX Metazoa_XXXX_sp.
Metazoa Mollusca Bivalvia NA NA NA
Metazoa Mollusca Bivalvia Protobranchia NA NA
Metazoa Mollusca Bivalvia Heteroconchia NA NA
Metazoa Mollusca Bivalvia Pectinoida NA NA
Metazoa Mollusca Cephalopoda Cephalopoda_X NA NA
Metazoa Mollusca Gastropoda Vetigastropoda NA NA
Metazoa Mollusca Gastropoda Neritopsina Depressigyra Depressigyra_sp.
Metazoa Mollusca Gastropoda Heterobranchia Rissoella_gastropoda Rissoella_rissoaformis
Metazoa Mollusca Gastropoda Vetigastropoda Vetigastropoda_X Vetigastropoda_X_sp.
Metazoa Mollusca Gastropoda Neritopsina Depressigyra NA
Metazoa Mollusca Gastropoda Caenogastropoda NA NA
Metazoa Mollusca NA NA NA NA
Metazoa Myxozoa Myxozoa_X Myxosporea Kudoa NA
Metazoa Myzostomida Myzostomida_X Myzostomida_XX Myzostoma NA
Metazoa Nematoda Chromadorea Chromadorea_X NA NA
Metazoa Nematoda Chromadorea Chromadorea_X Chromadorea_XX Chromadorea_XX_sp.
Metazoa Nematoda Chromadorea Chromadorea_X Leptolaimus Leptolaimus_sp.
Metazoa Nematoda Chromadorea NA NA NA
Metazoa Nematoda Enoplea Enoplea_X NA NA
Metazoa Nemertea Nemertea_X Nemertea_XX NA NA
Metazoa Nemertea Nemertea_X Nemertea_XX Nemertea_XXX Nemertea_XXX_sp.
Metazoa Platyhelminthes Turbellaria Catenulida NA NA
Metazoa Platyhelminthes Turbellaria Polycladida NA NA
Metazoa Platyhelminthes Turbellaria Acoelomorpha NA NA
Metazoa Platyhelminthes Turbellaria Rhabdocoela NA NA
Metazoa Platyhelminthes Turbellaria Prolecithophora Plagiostomum NA
Metazoa Platyhelminthes Turbellaria Seriata NA NA
Metazoa Platyhelminthes Turbellaria Prolecithophora NA NA
Metazoa Platyhelminthes Turbellaria Rhabdocoela Gyratrix NA
Metazoa Porifera Porifera_X Calcarea NA NA
Metazoa Porifera Porifera_X Hexactinellida NA NA
Metazoa Porifera Porifera_X Demospongiae NA NA
Metazoa Porifera Porifera_X Demospongiae Geodia NA
Metazoa Rotifera Rotifera_X Rotifera_XX NA NA
Metazoa Rotifera Rotifera_X Rotifera_XX Rotifera_XXX Rotifera_XXX_sp.
Metazoa Urochordata Urochordata_X Ascidiacea NA NA
Metazoa Urochordata Urochordata_X Appendicularia Oikopleura Oikopleura_dioica
Metazoa Urochordata Urochordata_X Ascidiacea Cyclosalpa NA
Metazoa NA NA NA NA NA
Opisthokonta_X Opisthokonta_XX Opisthokonta_XXX Opisthokonta_XXXX Opisthokonta_XXXXX Opisthokonta_XXXXX_sp.
NA NA NA NA NA NA

3.2 Stats on sequence data

# Number of ASVs
tmp <- asv_wtax %>% 
  filter(Supergroup == "Opisthokonta")
100*(length(unique(tmp$FeatureID))/length(unique(asv_wtax$FeatureID)))
## [1] 8.849113
# Number of sequences
100*(sum(tmp$value)/sum(asv_wtax$value))
## [1] 27.15345

Total number of ASVs across sites is 1587 - totaling to 8.8% of all ASVs recovered and 27% of all sequences.

3.3 Bar plots of metazoa: Phylum & Class

# head(asv_wtax)
metazoa_all_barplot <- asv_wtax %>% 
  filter(Supergroup == "Opisthokonta") %>%
  filter(Sample_or_Control == "Sample") %>% 
  # unite(SAMPLETYPE_2, SITE, SAMPLETYPE, sep = " ") %>% 
  group_by(SITE, SAMPLETYPE, Phylum) %>% 
  summarise(SUM_CLASS = sum(value)) %>% 
  # unite(PhylumClass, Phylum, Class, sep = "-") %>% 
  ggplot(aes(x = SITE, y = SUM_CLASS, fill = Phylum)) +
    geom_bar(stat = "identity", position = "fill", color = "white", stroke = 0.1) +
    theme_classic() +
  coord_flip() +
  facet_grid(SAMPLETYPE ~. , space = "free") +
  scale_fill_viridis(discrete = TRUE, option = "turbo") +
  labs(x = "", y= "Sequence relative abundance") +
  theme(legend.position = "bottom")
## `summarise()` has grouped output by 'SITE', 'SAMPLETYPE'. You can override using the `.groups` argument.
## Warning: Ignoring unknown parameters: stroke
ggplotly(metazoa_all_barplot)

Observations: At the phylum level, metazoa made up the most number of 18S sequences recovered. This was followed by Choanoflagellates in the background and plume environments, and then by fungi in the vent habitats.

3.3.1 to the class level

# head(asv_wtax)
metazoa_all_barplot_class <- asv_wtax %>% 
  filter(Supergroup == "Opisthokonta") %>%
  filter(Sample_or_Control == "Sample") %>% 
  # unite(SAMPLETYPE_2, SITE, SAMPLETYPE, sep = " ") %>% 
  group_by(SITE, SAMPLETYPE, Phylum, Class) %>% 
  summarise(SUM_CLASS = sum(value)) %>% 
  unite(PhylumClass, Phylum, Class, sep = "-") %>% 
  ggplot(aes(x = SITE, y = SUM_CLASS, fill = PhylumClass)) +
    geom_bar(stat = "identity", position = "fill", color = "white", stroke = 0.1) +
    theme_classic() +
  facet_grid(SAMPLETYPE ~. , space = "free") +
  coord_flip() +
  scale_fill_viridis(discrete = TRUE, option = "inferno") +
  labs(x = "", y= "Sequence relative abundance") +
  theme(legend.position = "bottom")
## `summarise()` has grouped output by 'SITE', 'SAMPLETYPE', 'Phylum'. You can override using the `.groups` argument.
## Warning: Ignoring unknown parameters: stroke
ggplotly(metazoa_all_barplot_class)

Observations: There’s a shift in the community from the background and plume habitats having higher relative abundances of Ctenophora and Cnidaria sequences and Chanoflagellates (especially in the plume!), to the diffuse flow fluid having a higher relativea bundance of Annelida, Mollusca, and Arthropoda. (things that settle?)

3.3.2 closer look at metazoa only

# head(asv_wtax)
metazoa_only_bar <- asv_wtax %>% 
  filter(Phylum == "Metazoa") %>%
  filter(Sample_or_Control == "Sample") %>% 
  # unite(SAMPLETYPE_2, SITE, SAMPLETYPE, sep = " ", remove = FALSE) %>% 
  group_by(SAMPLETYPE, SITE, Class) %>% 
  summarise(SUM_CLASS = sum(value)) %>% 
  # unite(PhylumClass, Phylum, Class, sep = "-") %>% 
  ggplot(aes(x = SITE, y = SUM_CLASS, fill = Class)) +
    geom_bar(stat = "identity", position = "fill", color = "white", stroke = 0.1) +
    theme_classic() +
  facet_grid(SAMPLETYPE ~. , space = "free") +
  coord_flip() +
  scale_fill_viridis(discrete = TRUE, option = "rocket") +
  labs(x = "", y= "Sequence relative abundance") +
  theme(legend.position = "bottom")
## `summarise()` has grouped output by 'SAMPLETYPE', 'SITE'. You can override using the `.groups` argument.
## Warning: Ignoring unknown parameters: stroke
ggplotly(metazoa_only_bar)
# head(asv_wtax)
metazoa_only_Order_bar <- asv_wtax %>% 
  filter(Phylum == "Metazoa") %>%
  filter(Sample_or_Control == "Sample") %>% 
  # unite(SAMPLETYPE_2, SITE, SAMPLETYPE, sep = " ", remove = FALSE) %>% 
  group_by(SAMPLETYPE, SITE, Class, Order) %>% 
  summarise(SUM_CLASS = sum(value)) %>% 
  unite(ClassOrder, Class, Order, sep = "-") %>%
  ggplot(aes(x = SITE, y = SUM_CLASS, fill = ClassOrder)) +
    geom_bar(stat = "identity", position = "fill", color = "white", stroke = 0.1) +
    theme_classic() +
  facet_grid(SAMPLETYPE ~. , space = "free") +
  coord_flip() +
  scale_fill_viridis(discrete = TRUE, option = "rocket") +
  labs(x = "", y= "Sequence relative abundance") +
  theme(legend.position = "bottom")
## `summarise()` has grouped output by 'SAMPLETYPE', 'SITE', 'Class'. You can override using the `.groups` argument.
## Warning: Ignoring unknown parameters: stroke
ggplotly(metazoa_only_Order_bar)

Observations: When we go to the ‘Order’ level for metazoa, we see that many of the taxa names end with **_X**. This means the level is unknown. In the case of the PR2 database, it is still unclear if this means it is because that level is mis-placed, or they didn’t curate the rest of the sequence?

I used V4 primers. We can explore the PR2 database more here: https://pr2database.github.io/pr2database/articles/pr2database.html

# install.packages(devtools)
# devtools::install_github("pr2database/pr2database")

4 Next steps?

  • Sort out database issue
  • Is this biogeography helpful?
  • Closer look at substrates at Gorda Ridge (larger project)
  • Paired samples with other amplicons?